8WP2 | pdb_00008wp2

MapSPARTA tetramer bound with guide-target

• PDB DOI: https://doi.org/10.2210/pdb8WP2/pdb
• NAKB: 8WP2
• EM Map EMD-37708: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/DNA/RNA
• Organism(s): Maribacter polysiphoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-08 Released: 2024-12-11 
• Deposition Author(s): Huang, P.P., Li, Z.X., Guo, L.J., Xiao, Y.B., Chen, M.R.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM Structure of MapSPARTA

Huang, P.P., Guo, L.J., Li, Z.X., Yan, P.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A4B4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 502.76 kDa 
• Atom Count: 31,544 
• Modeled Residue Count: 3,646 
• Deposited Residue Count: 4,020 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Piwi domain-containing protein	A, C, I, K	507	Maribacter polysiphoniae	Mutation(s): 0
UniProt
Find proteins for A0A316E3U6 (Maribacter polysiphoniae) Explore A0A316E3U6  Go to UniProtKB:  A0A316E3U6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TIR domain-containing protein	B, D, J, L	452	Maribacter polysiphoniae	Mutation(s): 0
UniProt
Find proteins for A0A316E683 (Maribacter polysiphoniae) Explore A0A316E683  Go to UniProtKB:  A0A316E683

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3')	E, G, M, O	21	Maribacter polysiphoniae

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	F, H, N, P	25	Maribacter polysiphoniae

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Huang, P.P., Li, Z.X., Guo, L.J., Xiao, Y.B., Chen, M.R.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	Nos.2018YFA0902000
Ministry of Science and Technology (MoST, China)	China	ZX-2021ZD0203404
National Natural Science Foundation of China (NSFC)	China	Nos. 32271330
National Natural Science Foundation of China (NSFC)	China	Nos. 32000889
National Natural Science Foundation of China (NSFC)	China	Nos. 31970547

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2025-06-18
  Changes: Data collection